📅CoVariants.org is now updated with data up to the 18th Feb! 📅
Plus! A new mutation has been added 😉
And we've had another few neat feature tweaks thanks to some great contributors!
1/6
Enough recent data has come through to push the graphs to the next 2-week mark (they're plotted by sequences per 2-week period to help avoid weekly jitters), so the most recent data point is the 8th Feb now (covering the period two weeks after this).
2/6
Linking with our recent preprint on the S:Q677 variants, S:Q677 is now included on CoVariants!
We can particularly see 677 showing up clearly in the USA 'Per Country' graphs.
Another change you'll notice on the 'Per Country' & 'Per Variant' pages is the addition of 'Select All' & 'Deselect all' options - making it a lot easier if you want to focus in on just a few things!
Thanks to jscaptures for the idea & @ivan_aksamentov for implementing it!
4/6
On the 'Per Variant' pages the the tool-tip ordering options are a little more intuitive, & links have been added to the plot titles to make it easy to go to that variant's page and read more!
And finally, also thanks to @jamesscottbrown, you can now mouse-over the mutation badges to find out exactly what amino-acid change from and to. Incredibly useful if, like me, you don't have all your amino-acids memorised!
As always, a big thanks to all contributors!
6/6
Just to add a twitter handle - jscaptures on github is @Jak0bsc on twitter!
• • •
Missing some Tweet in this thread? You can try to
force a refresh
Tweets haven't been happening as times get busy, but CoVariants.org is now updated to data from 15 Feb! Focal builds are in the oven 🥖
This update also includes some neat new improvements - let's take a quick look!
1/4
Thanks to @jamesscottbrown, pages are now a little tidier, with the link icons placed after the links!
Thanks to a suggestion by @theosanderson the proportion of 'other' variants on the 'Per Country' page are now grey - easier to see and label!
2/4
@ivan_aksamentov has helped greatly improve the 'Per Variants' page! Tool-tip legends now show the lines so you can see the difference between solid & dashed!
And you can now select what kind or order you'd like the legend to show - frequency or country!
We found the same #SARSCoV2 mutation at position 677 in Spike has appeared at least 7 times in US-focused clusters in the past few months. What have we seen, & what does it mean?
Sparked by @macroliter & @DDomman independently spotting a rise in Q677P mutants in New Mexico & Louisiana, we teamed up & started investigating!
We noticed an increase in both Q677H and Q677P mutants around the world and within the USA, in particular since autumn 2020.
2/17
On a S:Q677-focused Nextstrain build, it quickly became apparent that there were multiple separate branches where Q677 mutants had arisen independently. We focused in on those in the USA.
It's #WomenInSTEM day today! 👩🏻💻👩🏾⚕️👩🏿🎓👩🏽🔬
I'm terrified of making lists of Twitter names as I know I'll leave someone off.
But I want to express how absolutely inspired I have been by the many brilliant women I've had the opportunity to work with this year & throughout my career!🎉
I absolutely remember how important it was (and is!) to be able to see myself in women who were in positions I aimed to achieve. Representation matters *so much.*
It helps to break down the expectations & stereotypes we often unknowingly internalise & realise what's possible!
Just 1 anecdote:
The first time I heard a brilliant women scientist whom I admired matter-of-factly state that she was looking forward both to the conference 🗒️ /and/ to shoe-shopping 👠 in the city it was in was *a revelation* for me. 🤯
Let's take a quick look at some snapshots of what we can see in the latest data.
1/15
Important note: the S:N501 build is now being more significantly impacted by downsampling.
I'm working on addressing this, but in the meantime, suggest looking at the S:E484 build for 501Y.V2 & 501Y.V3 & checking out the CoV Lineages report! cov-lineages.org/global_report.…
2/15
Israel now has over 200 sequences in 501Y.V1 (B.1.1.7). The latest additions indicate separate introductions (mostly from a month or two ago) and a large and still-growing local cluster.
As well as the major variants of concern, we can spot a couple of other clusters stemming from an 'old' #SARSCoV2 clade, 19B (originating in late 2019).
19A & 19B haven't been around much since early 2020, as they were overtaken by 20A, B & C (which carry D614G).
2/5
However, a few branches of 19B seem to be popping back up again recently.
In the UK, we can see a recent cluster that's acquired S:E484K (along with other mutations in S).
I'm still getting a *lot* of media enquiries - more than I can even respond to! So here's some of my best tips for how to reach out to me to maximise your chances of success (though I imagine they're true of other scientists too!)
1/7
(Just as a disclaimer - even if you use all of these, I can't promise I write back, or that I can say yes. If emails slip off the 'front page' of my inbox they basically fall into a black hole 😬. And sometimes I just cannot take any more interviews, even great ones.)
2/7
1. Please tell me what time zone you're in!
If I want to say 'yes' that means a pencilled-in appointment goes into the calendar immediately - so I need to know when you're likely to be awake. If I have to email you to find out... it might not happen.
3/7